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GenotypeGVCFs output is empty gvcf file

KG_Fun_GenKG_Fun_Gen Member
edited March 2018 in Ask the GATK team

I ran java -Xmx48g -jar gatk/3.5-0/src/GenomeAnalysisTK.jar -T GenotypeGVCFs -R hg19/hg19.fa -V merged.240samples.chr22.gvcf.gz -o merged.jointGT.chr22.gvcf.gz

it got successfully completed

INFO 20:18:40,706 ProgressMeter - Total runtime 9474.26 secs, 157.90 min, 2.63 hours
[
INFO 17:40:45,466 HelpFormatter - --------------------------------------------------------------------------------
INFO 17:40:45,469 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
INFO 17:40:45,469 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 17:40:45,469 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 17:40:45,472 HelpFormatter - Program Args: -T GenotypeGVCFs -R hg19/hg19.fa -V merged.240samples.chr22.gvcf.gz -o merged.jointGT.chr22.gvcf.gz
INFO 17:40:45,476 HelpFormatter - Executing as [email protected] on Linux amd64; Java HotSpot(TM) 64-Bit
INFO 17:40:45,476 HelpFormatter - Date/Time: 2018/03/28 17:40:45
INFO 17:40:45,476 HelpFormatter - ----------------------------------

unfortunately my outputfile is empty
this is my empty output gvcf file

fileformat=VCFv4.2

ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">

FILTER=<ID=LowQual,Description="Low quality">

FILTER=<ID=PASS,Description="All filters passed">

FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">

FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">

FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">

FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">

FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another">

FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">

FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">

FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">

FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">

GATKCommandLine.GenotypeGVCFs=<ID=GenotypeGVCFs,Version=3.5-0-g36282e4,Date="Wed Mar 28 17:40:46 EDT 2018",Epoch=1522273246553,CommandLineOptions="analysis_type=GenotypeGVCFs input_file=[] show

GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.5-0-g36282e4,Date="Fri Dec 09 08:21:43 EST 2016",Epoch=1481289703015,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[

GATKCommandLine.SelectVariants=<ID=SelectVariants,Version=3.5-0-g36282e4,Date="Wed Mar 21 22:41:46 EDT 2018",Epoch=1521686506383,CommandLineOptions="analysis_type=SelectVariants input_file=[] s

GATKCommandLine=<ID=CombineGVCFs,CommandLine="CombineGVCFs --output merged..chr22.gvcf.gz --variant /scratch//meta-mer

GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive)

GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive)

GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive)

GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive)

GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive)

GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive)

GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive)

GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive)

GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive)

GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive)

GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive)

GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive)

GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive)

GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive)

GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive)

GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive)

GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive)

GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive)

GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive)

GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive)

GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive)

GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive)

GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive)

GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive)

GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive)

GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive)

GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive)

GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive)

GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive)

GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive)

GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive)

GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive)

GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive)

GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive)

GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive)

GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive)

GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive)

GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive)

GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive)

GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive)

GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive)

GVCFBlock46-47=minGQ=46(inclusive),maxGQ=47(exclusive)

GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive)

GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive)

GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive)

GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive)

GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive)

GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive)

GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive)

GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive)

GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive)

GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive)

GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive)

GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive)

GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive)

GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive)

GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive)

GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive)

GVCFBlock7-8=minGQ=7(inclusive),maxGQ=8(exclusive)

GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive)

GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive)

GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive)

GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive)

GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive)

GVCFBlock99-2147483647=minGQ=99(inclusive),maxGQ=2147483647(exclusive)

INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">

INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">

INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">

INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">

INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">

INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">

INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">

INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">

INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">

INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">

INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">

INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">

INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as list

INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as lis

INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">

INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">

INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">

INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">

INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">

INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">

bcftools_viewCommand=view -m2 -M2 meta-merged.1.chr22.gvcf.gz; Date=Tue Mar 27 12:42:50 2018

bcftools_viewVersion=1.7+htslib-1.7

contig=<ID=chr1,length=249250621,assembly=hg19>

contig=<ID=chr10,length=135534747,assembly=hg19>

contig=<ID=chr11,length=135006516,assembly=hg19>

contig=<ID=chr12,length=133851895,assembly=hg19>

contig=<ID=chr13,length=115169878,assembly=hg19>

contig=<ID=chr14,length=107349540,assembly=hg19>

contig=<ID=chr15,length=102531392,assembly=hg19>

contig=<ID=chr16,length=90354753,assembly=hg19>

contig=<ID=chr17,length=81195210,assembly=hg19>

contig=<ID=chr18,length=78077248,assembly=hg19>

contig=<ID=chr19,length=59128983,assembly=hg19>

contig=<ID=chr2,length=243199373,assembly=hg19>

contig=<ID=chr20,length=63025520,assembly=hg19>

contig=<ID=chr21,length=48129895,assembly=hg19>

contig=<ID=chr22,length=51304566,assembly=hg19>

contig=<ID=chr3,length=198022430,assembly=hg19>

contig=<ID=chr4,length=191154276,assembly=hg19>

contig=<ID=chr5,length=180915260,assembly=hg19>

contig=<ID=chr6,length=171115067,assembly=hg19>

contig=<ID=chr7,length=159138663,assembly=hg19>

contig=<ID=chr8,length=146364022,assembly=hg19>

contig=<ID=chr9,length=141213431,assembly=hg19>

contig=<ID=chrM,length=16571,assembly=hg19>

contig=<ID=chrX,length=155270560,assembly=hg19>

contig=<ID=chrY,length=59373566,assembly=hg19>

reference=/resources/hg19/hg19.fa

source=CombineGVCFs

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample_PFC_1130_A sample_PFC_1131_A sample_PFC_1132_A sample_PFC_1135_A sample_PFC_1136_A........

My input file

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT MSSM_PFC_1130_A MSSM_PFC_1131_A sample_PFC_1132_A sample_PFC_1135_A sample PFC_1136_A sample_PFC_1138_A sample_PFC_1139_A sample_PFC_11

chr22 1 . N . . END=16050000 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050001 . G . . END=16050002 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.
chr22 16050003 . T . . END=16050007 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.
chr22 16050008 . T . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050009 . A . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050010 . A . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050011 . G . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050012 . T . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050013 . C . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050014 . C . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050015 . C . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050016 . A . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050017 . G . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050018 . G . . END=16050019 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.
chr22 16050020 . C . . END=16050021 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.
chr22 16050022 . T . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050023 . C . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050024 . A . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050025 . G . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050026 . A . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050027 . A . . END=16050028 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.
chr22 16050029 . A . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050030 . G . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050031 . C . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050032 . T . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050033 . G . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050034 . T . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050035 . G . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050036 . A . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050037 . G . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050038 . A . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050039 . C . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050040 . C . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050041 . T . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
chr22 16050042 . T . . . GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 ./.:0:0:0:0
:

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